rs11251048

Positions:

• chr10-2078213-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435539.1(ENSG00000226694):​n.132-2584G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,112 control chromosomes in the GnomAD database, including 6,118 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6118 hom., cov: 33)
• Consequence: ENST00000435539.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435539.1	n.132-2584G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41658 AN: 151994 Hom.: 6118 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.269

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.274 AC: 41677 AN: 152112 Hom.: 6118 Cov.: 33 AF XY: 0.271 AC XY: 20147 AN XY: 74374

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.267

Alfa AF: 0.301 Hom.: 13420

Bravo AF: 0.286

Asia WGS AF: 0.224 AC: 777 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11251048; hg19: chr10-2120407;